Mercurial > repos > matthias > stacks2_sstacks
diff test-data/gstacks/gstacks.log @ 5:aef37afe214f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
| author | matthias |
|---|---|
| date | Wed, 27 Feb 2019 09:58:12 -0500 |
| parents | 2fb24beef45a |
| children | 4068ef4253ab |
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--- a/test-data/gstacks/gstacks.log Fri Jan 04 03:35:36 2019 -0500 +++ b/test-data/gstacks/gstacks.log Wed Feb 27 09:58:12 2019 -0500 @@ -1,24 +1,34 @@ -gstacks v2.2, executed 2018-11-27 19:48:29 -/home/berntm/miniconda3/envs/__stacks@2.2/bin/gstacks -P stacks_outputs -M /tmp/tmpSlCHrR/files/000/dataset_3.dat -t 1 --var-alpha 0.05 --gt-alpha 0.05 +gstacks v2.3b, executed 2019-02-22 12:51:51 +gstacks -P bam_inputs -M /tmp/tmpZcvUSM/files/000/dataset_3.dat -O stacks_outputs -t 1 --model marukilow --var-alpha 0.01 --gt-alpha 0.05 Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'. Configuration for this run: Input mode: denovo - Population map: '/tmp/tmpSlCHrR/files/000/dataset_3.dat' - Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam' + Population map: '/tmp/tmpZcvUSM/files/000/dataset_3.dat' + Input files: 2, e.g. 'bam_inputs/PopA_01.matches.bam' Output to: 'stacks_outputs/' - Model: marukilow (var_alpha: 0.05, gt_alpha: 0.05) + Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05) Reading BAM headers... Processing all loci... 20%... 50%... 100% -Input appears to be single-end (no paired-end reads were seen). + +Attempted to assemble and align paired-end reads for 3 loci: + 0 loci had no or almost no paired-end reads (0.0%); + 0 loci had paired-end reads that couldn't be assembled into a contig (0.0%); + For the remaining 3 loci (100.0%), a paired-end contig was assembled; + Average contig size was 204.3 bp; + 0 paired-end contigs overlapped the forward region (0.0%) + Mean overlap: -nanbp; mean size of overlapped loci after merging: -nan; + Out of 252 paired-end reads in these loci (mean 84.0 reads per locus), + 252 were successfuly aligned (100.0%); + Mean insert length was -nan, stdev: nan (based on aligned reads in overlapped loci). Genotyped 3 loci: - effective per-sample coverage: mean=21.0x, stdev=1.0x, min=20.0x, max=22.0x - mean number of sites per locus: 94.0 - a consistent phasing was found for 2 of out 2 (100.0%) diploid loci needing phasing + effective per-sample coverage: mean=31.0x, stdev=1.0x, min=30.0x, max=32.0x + mean number of sites per locus: 194.3 + a consistent phasing was found for 5 of out 5 (100.0%) diploid loci needing phasing gstacks is done.